Hi Aritz, I suggest you specify the width of the image in pixels rather than the pixelSize in Angstroms. save /path/image.tiff width 3000 supersample 3 The height will be automatically computed to match the aspect ratio. For most publication images you just want it to have enough pixels, for instance for a 7 inch wide image at 300 pixels per inch you would need a width of 2100 pixels (= 7 * 300). So 3000 is more than enough for most purposes. Also I suggest supersample 3 or less. Your supersample 4 renders 16 times the number of pixels (4x in x and y directions) and averages down to the requested. That is overkill -- you will not notice any difference except that it takes 16 times as long to save the image. In fact I doubt you could notice the difference with no supersampling if you save at 3000 pixels wide and display at a typical size (e.g. 7 inches wide on the screen). So I'd be more inclined to use save /path/image.tiff width 3000 and save yourself a bit of time. Tom

On Aug 2, 2024, at 11:24 AM, Ricardo Righetto via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Aritz,

To make sure that all images have the same size in the most strict way possible, you have to provide explicitly the width and height to the 'save' command. Additionally, you can use the 'windowsize' command first to have an idea of the aspect ratio that you want in the final figure (not strictly necessary, but I find it helpful). Here is an example where I clearly define windowsize, pixelsize and output image dimensions:

windowsize 1024 1024 camera ortho open tomos/50.mrc zoom pixelsize 1.0 vol #1 planes z,232 volume #1 color black sdLevel -2,1 color gray sdLevel 0,1 color white sdLevel 2,1 save Tomo50_slice232.png transparentBackground true width 4096 height 4096 supersample 3

Hope this helps!

Best wishes,

-- Ricardo Diogo Righetto

Em sex., 2 de ago. de 2024 às 16:14, Aritz Roa Eguiara via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> escreveu:

...

Dear Sir or Madam,

I am trying to make a default .cxc file that I can use to automatically save the view for publication. I am using the following:

save /path/image.tiff pixelSize 0.05 supersample 4

This turned out to give me the best files for most cases, but depending on the zoom I get different file sizes. Is there any way to have a standard command that gives me high quality images and that always have the same dimensions regardless of the zoom? I understand that the issue comes from the different pixel size of the zoom and that I am specifying a pixel size on the command, but when trying other alternatives I have not been successful to get proper images...

All the best,

Aritz

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